The veto drew praise from environment groups, The (Raleigh) News & Observer reported.
"Gov. Perdue stood up for our drinking water today," said Elizabeth Ouzts, Environment North Carolina state director. "She stood up for our air quality and our rural landscapes and against this dangerous approach to fracking."
In a statement, Perdue said she supports energy policies "that create jobs and lower costs for businesses and families."
"Our drinking water and the health and safety of North Carolina's families are too important; we can't put them in jeopardy by rushing to allow fracking without proper safeguards," she said.
The veto marked the Democratic governor's third veto in four days of Republican-backed legislation.
House Speaker Thom Tillis and Senate leader Phil Berger issued a joint statement in which they labeled the veto a "flip-flop."
They said the General Assembly had incorporated many of the governor's recommendations in a "bipartisan plan to begin developing the regulatory framework for affordable, clean energy alternatives."
"We are disappointed, but not surprised, that when decision time neared, she once again caved to her liberal base rather than support the promise of more jobs for our state," they said.
Overriding the veto would require a three-fifths majority vote in the House and Senate.
Fracking involves drilling into shale, then injecting water and chemicals to free trapped pockets of natural gas.